quantify
A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
Report generated on 2024-06-04, 12:23 CEST based on data in:
/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C01.lib1.Log.final.out/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C02.lib1.Log.final.out/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C03.lib1.Log.final.out/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C04.lib1.Log.final.out/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C05.lib1.Log.final.out/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C06.lib1.Log.final.out/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C06.lib1.Log.final.out/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C07.lib1.Log.final.out/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C08.lib1.Log.final.out/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C09.lib1.Log.final.out/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C10.lib1.Log.final.out/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C11.lib1.Log.final.out/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C12.lib1.Log.final.out/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C01.lib1.stats.tsv/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C02.lib1.stats.tsv/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C03.lib1.stats.tsv/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C04.lib1.stats.tsv/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C05.lib1.stats.tsv/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C06.lib1.stats.tsv/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C06.lib1.stats.tsv/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C07.lib1.stats.tsv/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C08.lib1.stats.tsv/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C09.lib1.stats.tsv/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C10.lib1.stats.tsv/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C11.lib1.stats.tsv/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C12.lib1.stats.tsv/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C01.lib1.flagstats.txt/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C02.lib1.flagstats.txt/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C03.lib1.flagstats.txt/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C04.lib1.flagstats.txt/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C05.lib1.flagstats.txt/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C06.lib1.flagstats.txt/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C06.lib1.flagstats.txt/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C07.lib1.flagstats.txt/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C08.lib1.flagstats.txt/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C09.lib1.flagstats.txt/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C10.lib1.flagstats.txt/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C11.lib1.flagstats.txt/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C12.lib1.flagstats.txt/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C01.lib1.idxstats.tsv/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C02.lib1.idxstats.tsv/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C03.lib1.idxstats.tsv/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C04.lib1.idxstats.tsv/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C05.lib1.idxstats.tsv/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C06.lib1.idxstats.tsv/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C06.lib1.idxstats.tsv/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C07.lib1.idxstats.tsv/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C08.lib1.idxstats.tsv/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C09.lib1.idxstats.tsv/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C10.lib1.idxstats.tsv/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C11.lib1.idxstats.tsv/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/results/quantify/star/E04C12.lib1.idxstats.tsv/maps/projects/mjolnir1/people/jpl786/goac_transcriptomics2/reports/config.yaml
General Statistics
| Sample Name | Error rate | Non-primary | Reads mapped | % Mapped | % Proper pairs | Total seqs | Reads mapped | % Aligned | M Aligned |
|---|---|---|---|---|---|---|---|---|---|
| E04C01.lib1 | 0.27% | 27.1M | 74.3M | 99.2% | 99.2% | 74.9M | 101.4M | 88.4% | 33.1M |
| E04C02.lib1 | 0.27% | 21.7M | 76.7M | 99.2% | 99.2% | 77.3M | 98.4M | 89.4% | 34.6M |
| E04C03.lib1 | 0.27% | 23.6M | 76.7M | 99.2% | 99.2% | 77.3M | 100.3M | 89.0% | 34.4M |
| E04C04.lib1 | 0.27% | 23.0M | 65.8M | 99.2% | 99.2% | 66.4M | 88.9M | 88.6% | 29.4M |
| E04C05.lib1 | 0.25% | 24.5M | 73.0M | 99.3% | 99.3% | 73.5M | 97.5M | 88.9% | 32.7M |
| E04C06.lib1 | 0.35% | 11.9M | 45.6M | 99.2% | 99.2% | 46.0M | 57.5M | 89.8% | 20.6M |
| E04C07.lib1 | 0.24% | 27.0M | 87.7M | 99.3% | 99.3% | 88.4M | 114.7M | 89.2% | 39.4M |
| E04C08.lib1 | 0.27% | 24.3M | 75.3M | 99.1% | 99.1% | 76.0M | 99.6M | 88.9% | 33.8M |
| E04C09.lib1 | 0.27% | 20.8M | 72.1M | 99.2% | 99.2% | 72.6M | 92.8M | 89.1% | 32.4M |
| E04C10.lib1 | 0.27% | 26.3M | 72.0M | 99.2% | 99.2% | 72.6M | 98.4M | 88.4% | 32.1M |
| E04C11.lib1 | 0.28% | 24.6M | 68.6M | 99.2% | 99.2% | 69.1M | 93.1M | 88.5% | 30.6M |
| E04C12.lib1 | 0.27% | 28.0M | 75.5M | 99.3% | 99.3% | 76.1M | 103.5M | 88.4% | 33.6M |
Samtools
1.20
Samtools is a suite of programs for interacting with high-throughput sequencing data.DOI: 10.1093/bioinformatics/btp352.
Percent mapped
Alignment metrics from samtools stats; mapped vs. unmapped reads vs. reads mapped with MQ0.
For a set of samples that have come from the same multiplexed library, similar numbers of reads for each sample are expected. Large differences in numbers might indicate issues during the library preparation process. Whilst large differences in read numbers may be controlled for in downstream processings (e.g. read count normalisation), you may wish to consider whether the read depths achieved have fallen below recommended levels depending on the applications.
Low alignment rates could indicate contamination of samples (e.g. adapter sequences), low sequencing quality or other artefacts. These can be further investigated in the sequence level QC (e.g. from FastQC).
Reads mapped with MQ0 often indicate that the reads are ambiguously mapped to multiple locations in the reference sequence. This can be due to repetitive regions in the genome, the presence of alternative contigs in the reference, or due to reads that are too short to be uniquely mapped. These reads are often filtered out in downstream analyses.
Alignment stats
This module parses the output from samtools stats. All numbers in millions.
Flagstat
This module parses the output from samtools flagstat. All numbers in millions.
Mapped reads per contig
The samtools idxstats tool counts the number of mapped reads per chromosome / contig. Chromosomes with < 0.1% of the total aligned reads are omitted from this plot.
STAR
STAR is an ultrafast universal RNA-seq aligner.DOI: 10.1093/bioinformatics/bts635.
Alignment Scores
Software Versions
Software Versions lists versions of software tools extracted from file contents.
| Software | Version |
|---|---|
| Samtools | 1.20 |